Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
DNMT3B

Cell type

Cell type Class
Epidermis
Cell type
Keratinocytes
MeSH Description
Epidermal cells which synthesize keratin and undergo characteristic changes as they move upward from the basal layers of the epidermis to the cornified (horny) layer of the skin. Successive stages of differentiation of the keratinocytes forming the epidermal layers are basal cell, spinous or prickle cell, and the granular cell.

Attributes by original data submitter

Sample

source_name
Differentiated Keratinocytes
passage
2
tissue
Foreskin
chip-antibody
Dnmt3b (Novus Biotechnology. Cat: NB100-266)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
EpiSC and differentiated keratinocytes were trypsinized and crosslinked in 1% formaldehyde (FA) for 10 min at room temperature (RT). For ChIPs from EBs, crosslinking was performed for 30 min at RT in 4% FA. Crosslinking was quenched with 0.125 M glycine. Pelleted cells were lysed in 1 ml ChIP buffer and sonicated for 15 min in a Bioruptor (Diagenode). Soluble material was quantified by Bradford assays. To immunoprecipitate transcription factors, 2000 mg of protein and 100 mg of immunoprecipitated histone/histone modifications were used. Antibodies (10ug for DnmtA/3B and 3ug for histone modifications) were incubated overnight with the chromatin. Immunocomplexes were recovered with 30 ul of protein A bead slurry (Healthcare. Cat # 17-5280-01). Immunoprecipitated material was washed three times with low salt buffer and one time with high salt buffer. DNA complexes were decrosslinked at 65_C overnight, and DNA was then eluted in 50 ul of water using the PCR purification kit (QIAGEN)

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
41038018
Reads aligned (%)
82.4
Duplicates removed (%)
15.0
Number of peaks
1611 (qval < 1E-05)

hg38

Number of total reads
41038018
Reads aligned (%)
84.3
Duplicates removed (%)
13.7
Number of peaks
1644 (qval < 1E-05)

Base call quality data from DBCLS SRA